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Hello,
First, my obligatory brown-nosing: I love phyloseq and have been getting pretty intimate with it the past week. I've been trying to transition over to using R for my informatics work because …
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We're seeing some fragmentation on workflows due to switches in technologies (PacBio, Shoreline, Loop, etc) that a migration to DSL2 would help tremendously. This is a simple tracker to plot a course…
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Hi,
I generated the phyloseq object from DADA2 pipeline, and when calculating the prevalence using this code:
`prevelancedf = apply(X = otu_table(ps),
MARGIN = 1,
…
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Hello, I am wondering how can I extract the sequence variant names (named as ASV1, ASV2, ASV3...) together with their sequences from the refseq slot? Is there an easy way to extract the data from the …
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Hello. I have succesfully ran contributional alpha diversity on my data. When I run the beta diversity script, the output generated files are empty. I ran the code using the default contributions outp…
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Hi DADA2 developer,
I have a high-level conceptual question - I've seen people clustering ASVs into OTUs at certain similarity threshold for various purposed. How is that different from directly us…
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Due to the lack of a specification on that aspect, our processors have no or no uniform way to inform the user whether or not a GPU device is used (or even parameterise which one to prefer). Here's th…
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### Is your feature request related to a specific problem?
One common challenge to memorized secrets (side note, use a password manager!) is that they are likely to be forgotten.
Our login scree…
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Hi,
I have been reading the literature regarding this topic, and the video from Pat Schloss showed that sequencing depth is still influencing the estimation in `breakaway`.
[https://www.youtube…
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### 🚀 The feature, motivation and pitch
Introduce PyG lifetime benchmarks with a dashboard 🚀 (using https://github.com/airspeed-velocity/asv)
## Motivation
There are quite a number of benchma…